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A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any i...

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Detalles Bibliográficos
Autores principales: Nunez-Iglesias, Juan, Blanch, Adam J., Looker, Oliver, Dixon, Matthew W., Tilley, Leann
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816961/
https://www.ncbi.nlm.nih.gov/pubmed/29472997
http://dx.doi.org/10.7717/peerj.4312
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author Nunez-Iglesias, Juan
Blanch, Adam J.
Looker, Oliver
Dixon, Matthew W.
Tilley, Leann
author_facet Nunez-Iglesias, Juan
Blanch, Adam J.
Looker, Oliver
Dixon, Matthew W.
Tilley, Leann
author_sort Nunez-Iglesias, Juan
collection PubMed
description We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.
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spelling pubmed-58169612018-02-22 A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton Nunez-Iglesias, Juan Blanch, Adam J. Looker, Oliver Dixon, Matthew W. Tilley, Leann PeerJ Biochemistry We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions. PeerJ Inc. 2018-02-15 /pmc/articles/PMC5816961/ /pubmed/29472997 http://dx.doi.org/10.7717/peerj.4312 Text en ©2018 Nunez-Iglesias et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biochemistry
Nunez-Iglesias, Juan
Blanch, Adam J.
Looker, Oliver
Dixon, Matthew W.
Tilley, Leann
A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
title A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
title_full A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
title_fullStr A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
title_full_unstemmed A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
title_short A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
title_sort new python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
topic Biochemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816961/
https://www.ncbi.nlm.nih.gov/pubmed/29472997
http://dx.doi.org/10.7717/peerj.4312
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